.. index:: About


About
=====

Like other pipeline/workflow managers, Bio_pype improves
scalability and reproducibility while simplifying daily bioinformatics 
analyses.

Bio_pype provides a modular framework for building analysis pipelines
through three major components: Snippets, Pipelines, and Profiles.

Snippets
--------

Snippets are the basic building blocks of pipelines. They act as wrappers
that handle:
- Command-line argument packaging
- Input preprocessing
- Tool execution
- Output management

Most importantly, snippets provide a uniform interface that allows Bio_pype
to connect multiple analysis steps into a complete pipeline.

Pipelines
---------

A pipeline represents a series of analysis steps. In Bio_pype, pipelines
are defined using YAML files that specify:
- Which snippets to run
- The order of execution
- How snippets connect and share data
- Resource requirements

Profiles
--------

Profiles manage the execution environment by specifying:
- Locations of reference data and genomes
- Software installations and versions
- System resource configurations
- Environment modules and containers

This allows pipelines to run consistently across different systems while
maintaining their logical structure.

Registry
--------

The workflow registry is a package manager for bioinformatics workflows. It allows
you to:

- **Discover** available workflows: ``pype registry search``
- **Install** specific versions: ``pype registry install qc==2025.12.31-1``
- **Activate** a workflow for use: set ``PYPE_MODULES`` to the installed path
- **Publish** and distribute your own workflows

Workflows are distributed via git repositories, versioned, and can be updated
while preserving any local customizations made to previous versions.